Microarray  Workflow (big)


The EBRI-CNR genomics facility was initiated to use high-density microarrays for investigating gene expression profiling of the Nervous System. Currently it provides gene expression services for the reasearch community.

Agilent Technologies generously donated a two lasers microarray scanner. The facility is jointly supported by EBRI and CNR to provide specialist genomics resources for research projects both within and out of this research centre. Ongoing research projects involve mRNA expression profiling in neurodegenerative disease models and in memory and learning processes in the mammalian motor cortex.

The facility is fully equipped for all aspects of microarrays and Real Time PCR experiments, including RNA sample analysis.
We are also able to design custom Agilent microarrays.

Here are the main operations performed in the laboratory:

  • RNA extraction
  • RNA quality check
  • cRNA labelling
  • cRNA hybridization on microarrays chips
  • extraction of gene expression data from microarrays
  • gene expression quantification with Real Time PCR
  • data analysis

Sample RNA is first quality checked using the microfluidic platform Agilent Bioanalyzer 2100, that can also be used to analyze DNA, proteins and cells. Post labeling efficiency is quantified by Nanodrop ND-1000 prior to hybridization of samples to the chips. Post-hybridization image acquisition is accomplished using the Agilent scanner, equipped two lasers (532 nm and 635 nm) and a 48 slide auto-sampler carousel. Data extraction from the images is accomplished Agilent Feature Extraction software. Data analysis is performed using Agilent GeneSpring, Bioconductor, Microsoft Excel with addins, SAM, other online tools.

More details

Group Components

Mara D´Onofrio (EBRI) Coordinator Scientist

Armando Felsani  Scientist

Ivan Arisi (EBRI) Bioinformatics Scientist

Rossella Brandi (EBRI) Scientist


D´Onofrio, M., Arisi, I., Brandi, R., Di Mambro, A., Felsani, A., S, C. & Cattaneo, A. Early inflammation and immune response mRNAs in the brain of AD11 anti−NGF mice. Neurobiol Aging (2010). doi:10.1016/j.neurobiolaging.2009.05.023.

Lagostena, .L, Marcelo Rosato-Siri,M., D’Onofrio, M., Brandi, R.,, Arisi, I.C and Capsoni, S., Franzot, J., Cattaneo, A., and Cherubini, E. In the Adult Hippocampus, Chronic Nerve Growth Factor Deprivation Shifts GABAergic Signaling from the Hyperpolarizing to the Depolarizing Direction. The Journal of Neuroscience, January 20, 2010 • 30(3):885– 893.

Barbato C., Arisi I., Frizzo M.E., Brandi R., Da Sacco L. and Masotti A. “Computational Challenges in miRNA Target Predictions: To Be or Not to Be a True Target?”, J Biomed Biotechnol, vol. 2009, 2009:803069. Epub 2009 Jun 17.

D’Onofrio, M., Ambrosini, A., Di Mambro, A., Arisi, I., Santorelli, F.M., Grieco, G.S. Nicoletti F., Nappi, G., Pierelli, F., Schoenenh, F., Buzzi M.G. The interplay of two single nucleotide polymorphisms in the CACNA1A gene may contribute to migraine susceptibility. Neuroscience Letters 453 (2009) 12–15.